I tried to install Python 3.6 and got 1000s of lines of conflicts, and python version still returns 3.8. when I switch back to my Qiime environment to install Aldex2, I get an error. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Replacing broken pins/legs on a DIP IC package. Error in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]) : there is no package called 'data.table' Error: package or namespace load failed for 'DESeq2' Tried installing the missing package: R version 3.6.1 (2019-07-05) Error: package or namespace load failed for 'DESeq2 - Bioconductor We've tried this - and can replicate this issue on a completely new install with no existing package installs. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( I can download DESeq2 using, User Agreement and Privacy And finally, install the problem packages, perhaps also DESeq2. I tried following the instructions for 2019.7 as well and I am getting the same error. 1. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. How do you ensure that a red herring doesn't violate Chekhov's gun? Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) R DESeq2 - By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Not the answer you're looking for? [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in I am also encountering a set of similar (although possible totally unrelated) issue with other packages, RStudio provides the following warning every startup, library(devtools) gives the following errors, Someone on twitter asked for the results of packageDescription("rlang"). 9543 Abort trap: 6 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}, The downloaded source packages are in If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : 4. "After the incident", I started to be more careful not to trip over things. if (!require("BiocManager", quietly = TRUE)) Platform: x86_64-w64-mingw32/x64 (64-bit) Are there tables of wastage rates for different fruit and veg? I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. Thanks for contributing an answer to Stack Overflow! More info about Internet Explorer and Microsoft Edge. To resolve this error, install the required package as a cluster-installed library. I noticed that you are trying to install qiime2-2019.4, this may not work as ALDEx2 was made for qiime2-2019.7 as outlined here, up to and including the versions I mentioned earlier. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. Open Source Biology & Genetics Interest Group. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. rev2023.3.3.43278. I would recommend installing an older version of QIIME 2 for this plugin to work. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. In install.packages() : If it fails, required operating system facilities are missing. Making statements based on opinion; back them up with references or personal experience. .onLoad failed in loadNamespace() for 'rlang', details: I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Is there anything I can do to speed it up? I have tried your suggestion and also updating the packages that command indicates. C:\R\R-3.4.3\library). CRAN: https://mirrors.sjtug.sjtu.edu.cn/cran/, Bioconductor version 3.12 (BiocManager 1.30.17), R 4.0.3 (2020-10-10), Old packages: 'cli', 'dplyr', 'igraph', 'MASS', 'ps', 'RSQLite', 'testthat', 'tibble', package locift is not available for Bioconductor version '3.12', A version of this package for your version of R might be available elsewhere,see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages. R version 4.0.1 (2020-06-06) This is the same answer I wrote in a comment to Hack-R I just wanted to post a separate answer: What I did was - uninstalled everything (RTools then RStudio thenR and also I deleted the R directory because it still had all the previous libraries) I did this in order to eliminate any chance that something was corrupt. While a notebook is attached to a cluster, the R namespace cannot be refreshed. Glad everything is finally working now. Any other suggestion? Likely what happened is that you managed to install a dependency, but then corrupted your installation by removing one of it's dependencies (manually via remove.packages(), or changing .libPaths(), or? Follow Up: struct sockaddr storage initialization by network format-string. Why are physically impossible and logically impossible concepts considered separate in terms of probability? + ), update = TRUE, ask = FALSE) Thank you @hharder. [40] assertthat_0.1 rpart_4.1-10 nnet_7.3-12, It should not be necessary (R should take care of loading dependencies) but try installating data.table also. If you try loading the DEseq2 library now, that might work. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Idk, but the issue came up from using installations from within R/Rstudio, and maybe it will never happen if we use just, @NikitaVlasenko you should be able to point Rstudio to the, We've added a "Necessary cookies only" option to the cookie consent popup, DESeqDataSetFromTximport invalid rownames length, deseq2 model design : Different gene output, deseq2 single factor design output interpretation. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 Is there anyone the same as mine error while loading library(DESeq2)? R version 3.6.3 (2020-02-29) + "htmlTable", "xfun" To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Error: package or namespace load failed for 'DESeq2' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): there is no package called 'locfit' 0 cbravo11 0 @e0025e70 Last seen 10 months ago United States I installed DESeq2 using this code: [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 Just realize that I need to write the script "library("DESeq2")" before I proceed. library (olsrr) - Error - General - RStudio Community Use of this site constitutes acceptance of our User Agreement and Privacy A place where magic is studied and practiced? trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 Running under: macOS Catalina 10.15.3, Matrix products: default sessionInfo() I again tried the installation with biocLite but was met with errors of missing packages (or the installation was ok and the when I tried loading the DESeq2 library I was met with missing packages errors) so I changed the CRAN mirror in RStudio. Is there a proper earth ground point in this switch box? [Note I have now updated to 3.5.1 and 1.1.453 and am still experiencing the issues below with the exception of the "built under R version 3.5.1" warning messages], I have installed the rlang package using install.packages("rlang") without encountering any issues but when I attempt to load the package I get the following error, Error: package or namespace load failed for rlang: ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR I guess that means we can finally close this issue. To learn more, see our tips on writing great answers. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. call: dots_list() This can take several minutes. The nature of simulating nature: A Q&A with IBM Quantum researcher Dr. Jamie We've added a "Necessary cookies only" option to the cookie consent popup. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. running multiple versions of the same package, keeping separate libraries for some projects). [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 I tried the installation with biocLite again and was met with missing packages again (or the installation was ok and the when I tried loading the DESeq2 library I was met with missing packages errors, I don't remember) BUT!!! Bioconductor - DESeq2 [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 Then I reinstalled R then Rstudio then RTools. library ("DESeq2") Error: package or namespace load failed for 'DESeq2' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): there is no package called 'Hmisc' Installing Hmisc as suggested above did not solve the issue. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 Just updated my previous R to 4.01 and now I cant load DESeq2. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 I was assuming that to be the case. Warning message: Whats the grammar of "For those whose stories they are"? This includes any installed libraries. rev2023.3.3.43278. Now loading the DESeq2 library (Errors): Because I already installed >10 packages by hand I assume the solution is not to keep installing the missing packages because those packages will have more missing packages and more and more and I won't get out of this loop. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. nnet, spatial, survival. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Traffic: 307 users visited in the last hour, https://cran.rstudio.com/src/contrib/htmlTable_2.1.0.tar.gz', https://wbc.upm.edu.my/cran/src/contrib/PACKAGES'. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. Running under: macOS Sierra 10.12.6. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. library(caret) namespace load failed Object sigma not When an R package depends on a newer package version, the required package is downloaded but not loaded. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, to one of the following locations: https://code.bioconductor.org/browse/DESeq2/, https://bioconductor.org/packages/DESeq2/, git clone https://git.bioconductor.org/packages/DESeq2, git clone git@git.bioconductor.org:packages/DESeq2. - the incident has nothing to do with me; can I use this this way? Are you sure the R you're running from the command line is installed through Anaconda as well? :), BiocManager::install("locift") I would like to install DESeq2 for DE analysis. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE I'd take a look at need, to see if there are any insights to be had, so that you can correct the root problem rather than having to do this procedure with other packages. Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Citation (from within R, enter citation ("DESeq2") ): Installation To install this package, start R (version "4.2") and enter: if (!require ("BiocManager", quietly = TRUE)) install.packages ("BiocManager") BiocManager::install ("DESeq2") For older versions of R, please refer to the appropriate Bioconductor release . From the console install.packages ("rlang") should fix this. Styling contours by colour and by line thickness in QGIS. If I run install.packages(GenomeInfoDb) from R console, it is telling me that the package is not available for R version 3.5.1. Traffic: 307 users visited in the last hour, I am new to all this! Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. Why do academics stay as adjuncts for years rather than move around? Already on GitHub? Installing DESeq2 Error: no package called GenomeInfoDbData, https://bioconductor.org/packages/3.11/data/annotation/src/contrib/GenomeInfoDbData_1.2.3.tar.gz, https://cran.rstudio.com/bin/macosx/contrib/4.0/RcppArmadillo_0.9.880.1.0.tgz, https://cran.rstudio.com/bin/macosx/contrib/4.0/survival_3.1-12.tgz. It only takes a minute to sign up. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? Browse other questions tagged, Start here for a quick overview of the site, Detailed answers to any questions you might have, Discuss the workings and policies of this site. Connect and share knowledge within a single location that is structured and easy to search. Use this. When you install and load some libraries in a notebook cell, like: While a notebook is attached to a cluster, the R namespace cannot be refreshed. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 How can we prove that the supernatural or paranormal doesn't exist? I hope you can see something I can't see and help me solving this issue. Do I need a thermal expansion tank if I already have a pressure tank? If you have a query related to it or one of the replies, start a new topic and refer back with a link. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: 9. I tried to get a whole new environment and install an old version of Qiime but I still got a ton of conflicts and it didnt install. [5] IRanges_2.8.1 S4Vectors_0.12.1 Installing package(s) 'GenomeInfoDbData' Give up and run everything from the "permitted" library location (e.g. 2. in your system, start R and enter: Follow ERROR: lazy loading failed for package Hmisc If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. Disconnect between goals and daily tasksIs it me, or the industry? Platform: x86_64-apple-darwin13.4.0 (64-bit) I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. binary R install.packages("XML",type="binary") install.packages("RCurl",type="binary") R"had non-zero exit status" - (zhihu.com) 1 R APP "" wx 1 1.1W 4 0 Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called GenomeInfoDbData [7] edgeR_3.16.5 limma_3.30.12 Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: Your best bet would be to download the package source code and change the R version and install manually if you wanted the most recent version of locfit to install on your computer. "After the incident", I started to be more careful not to trip over things. How to use Slater Type Orbitals as a basis functions in matrix method correctly? MathJax reference. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Fortunately I was able to solve it by doing things from several suggested solutions. privacy statement. Citation (from within R, C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages March 1, 2023, 8:52pm DESeq2 - I can't get the library to load - Bioconductor Content type 'application/zip' length 386703 bytes (377 KB) a, There are binary versions available but the source versions are later: If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Error: package or namespace load failed for 'olsrr' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): there is no package called 'zip' mara May 25, 2021, 12:49pm #2 It looks like you need a package that it depends on. Why is there a voltage on my HDMI and coaxial cables? Assuming that your conda environment name is renv, try running this in the terminal: This should open up the Rstudio interface, like normal, but using everything defined in your renv environment. In the Bioconductor realm, I would then check that package versions are consistent with the version of Bioconductor in use, and would ask more Bioconductor-related questions on the Bioconductor support site. install.packages("BiocManager"), I get this error: Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) I installed the package successfully with conda, but Rstudio is apparently does not know about it. Start R to confirm they are gone. Sounds like there might be an issue with conda setup? Any suggestions would be greatly appreciated. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called data.table @artembus Sounds like it was a ton of work! Sign in Have a question about this project? I'm running into some bad problems installing and using the DESeq2 package for R. I freshly installed R 3.3.1 and Rstudio 0.99.903 on Win7. Use of this site constitutes acceptance of our User Agreement and Privacy library(caret) namespace load failed Object sigma not found caret , . I also tried something I found on google: but the installation had errors too, I can write them here if needed. May I know is there any other approach I can try? I even tried BiocManager::install("XML") but all failed as shown below. Working with my work IT department we have now tied this to custom permissions on my workstation that mean that R packages can only be run to pre-specified libraries (in my case "C:\R\R-3.4.3\library"). But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. Running under: Windows 10 x64 (build 18362), locale: The package has place the R version constraint. package xfun successfully unpacked and MD5 sums checked How to use Slater Type Orbitals as a basis functions in matrix method correctly? I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. [69] tidyselect_1.0.0. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Is a PhD visitor considered as a visiting scholar?